Contacts of the helix formed by residues 1622 - 1628 (chain C) in PDB entry 5JCZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET1622 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1618C ILE* 3.5 25.6 - - - +
1619C LEU* 2.9 14.6 + - + +
1621C PRO* 1.3 81.8 - - + +
1623C ILE* 1.3 59.5 + - + +
1624C VAL 3.7 0.7 - - - -
1625C SER 3.8 1.1 + - - -
1626C GLY* 2.9 28.6 + - - -
1657C TYR* 3.7 40.6 - - + +
1661C SER* 3.3 48.7 - - - +
1662C ILE* 3.7 13.9 - - + +
1665C GLN* 4.2 25.4 - - + +
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Residues in contact with ILE1623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1619C LEU* 3.3 21.8 - - + +
1620C GLN* 3.5 3.1 + - - +
1621C PRO 3.5 1.4 - - - -
1622C MET* 1.3 76.4 - - + +
1624C VAL* 1.3 61.4 + - - +
1627C MET* 2.6 45.1 + - + +
1662C ILE* 4.2 10.1 - - + -
1693C ILE* 3.6 13.5 - - + +
1694C ILE* 3.6 37.9 - - + +
1697C ILE* 3.6 39.5 - - + -
1698C THR* 3.4 25.4 - - - +
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Residues in contact with VAL1624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1620C GLN* 4.8 4.1 + - - +
1621C PRO 5.1 1.2 + - - +
1623C ILE* 1.3 76.6 - - - +
1625C SER* 1.3 62.9 + - - +
1628C LEU* 3.1 27.9 + - + +
1629C GLU* 3.1 21.0 + - - +
1697C ILE* 4.0 11.2 - - + -
1698C THR* 6.2 0.4 - - - +
1701C ASN* 3.4 35.0 - - - +
1705C ARG* 3.4 28.9 - - - +
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Residues in contact with SER1625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1621C PRO 5.0 3.7 + - - -
1622C MET 3.8 7.3 + - - -
1623C ILE 3.3 0.2 - - - -
1624C VAL* 1.3 82.0 - - - +
1626C GLY* 1.3 58.9 + - - +
1629C GLU* 3.8 20.0 + - - +
1630C HIS* 2.9 32.2 + - - +
1656C THR* 2.8 20.7 + - - -
1657C TYR* 2.6 33.5 + - - -
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Residues in contact with GLY1626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1622C MET 2.9 19.2 + - - -
1623C ILE 3.7 0.2 - - - -
1625C SER* 1.3 79.0 - - - +
1627C MET* 1.3 61.7 + - - +
1630C HIS* 4.6 8.1 + - - +
1657C TYR 3.4 12.1 + - - -
1658C THR* 3.7 16.4 - - - -
1659C LEU* 3.7 16.5 + - - +
1662C ILE* 4.0 6.5 - - - -
1720C ASN* 3.8 8.5 + - - -
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Residues in contact with MET1627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1623C ILE* 2.6 30.6 + - + +
1626C GLY* 1.3 71.9 - - - -
1628C LEU* 1.3 64.5 + - + +
1630C HIS 5.4 0.7 - - - -
1659C LEU* 3.9 17.9 - - - -
1662C ILE* 4.0 10.8 - - + -
1694C ILE* 4.0 15.3 - - + -
1698C THR* 3.6 32.3 - - + +
1716C GLN* 4.7 1.7 - - - +
1717C ILE* 4.3 10.6 - - + +
1720C ASN* 2.8 50.0 + - + +
1721C VAL* 4.2 15.3 - - + -
1724C LEU* 4.1 19.3 - - + -
1745C LEU* 4.3 7.4 - - + -
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Residues in contact with LEU1628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1624C VAL* 3.1 17.0 + - + +
1626C GLY 3.5 0.4 - - - -
1627C MET* 1.3 88.6 - - + +
1629C GLU* 1.3 58.2 + - + +
1630C HIS 3.5 5.5 + - - +
1698C THR* 3.7 24.2 - - + +
1701C ASN* 3.6 34.1 - - + -
1702C LEU* 4.4 7.9 - - + +
1705C ARG* 4.8 3.1 - - - +
1708C MET* 3.9 28.7 - - + -
1713C LYS* 2.4 39.3 + - + +
1716C GLN* 4.8 3.0 - - - +
1717C ILE* 3.6 32.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il